The study assessed the genetic variability and the possibility of Scots pine regeneration in marshy forest. The genetic parameters were determined using the ISSR technique. The relationships between herbaceous plants, pine regeneration density, and their genetic variability were determined. On average, per 1 m2, three regenerated pine seedlings with a mean height of 27.56 cm were inventoried. Based on genetic analysis, it was found that the proportion of polymorphic loci was 60.46%. The average number of alleles at the locus was 1.345, and the effective number of alleles at the locus was 1.345. The values of the expected heterozygosity and Shannon index were 0.200 and 0.301, respectively. No species competing with pine regeneration were found. A significantly negative correlation of the number of pine regenerations with the area covered with an herbaceous plant layer and tree canopy closure was found. There was a relation to the insufficient amount of light under the stand canopy. In conclusion, the condition of marshy forests was satisfactory and the genetic variability of pine seedlings was moderate. The vegetation was typical for this habitat, but the significant presence of dry habitat species could indicate the beginning of habitat drainage. It seemed that the amount of light under the stand canopy was insufficient. Nevertheless, more light probably reached the inside of the stand in the terminal stage, as a result of upper layer tree separation, which in turn may facilitate the effective regeneration of Scots pine in this habitat.